HEADER RNA 28-JUL-10 2L1F TITLE STRUCTURE OF A CONSERVED RETROVIRAL RNA PACKAGING ELEMENT BY NMR TITLE 2 SPECTROSCOPY AND CRYO-ELECTRON TOMOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (65-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (66-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS; SOURCE 4 ORGANISM_TAXID: 11801; SOURCE 5 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 6 RNA POLYMERASE; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS; SOURCE 10 ORGANISM_TAXID: 11801; SOURCE 11 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 12 RNA POLYMERASE KEYWDS RNA, RETROVIRUS, PACKAGING, CRYO-ET EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.F.SUMMERS,R.N.IROBALIEVA,B.TOLBERT,A.SMALLS-MANTY,K.IYALLA, AUTHOR 2 K.LOELIGER,V.D'SOUZA,H.KHANT,M.SCHMID,E.GARCIA,A.TELESNITSKY,W.CHIU, AUTHOR 3 Y.MIYAZAKI REVDAT 4 01-MAY-24 2L1F 1 REMARK REVDAT 3 05-FEB-20 2L1F 1 SEQADV REVDAT 2 08-DEC-10 2L1F 1 JRNL REVDAT 1 27-OCT-10 2L1F 0 JRNL AUTH Y.MIYAZAKI,R.N.IROBALIEVA,B.S.TOLBERT,A.SMALLS-MANTEY, JRNL AUTH 2 K.IYALLA,K.LOELIGER,V.D'SOUZA,H.KHANT,M.F.SCHMID,E.L.GARCIA, JRNL AUTH 3 A.TELESNITSKY,W.CHIU,M.F.SUMMERS JRNL TITL STRUCTURE OF A CONSERVED RETROVIRAL RNA PACKAGING ELEMENT BY JRNL TITL 2 NMR SPECTROSCOPY AND CRYO-ELECTRON TOMOGRAPHY. JRNL REF J.MOL.BIOL. V. 404 751 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20933521 JRNL DOI 10.1016/J.JMB.2010.09.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED AND REFINED REMARK 3 WITH CYANA USING THE AMBER RESIDUE LIBRARY. UPPER-LIMIT DISTANCE REMARK 3 RESTRAINTS OF 2.7 , 3.3 AND 5.0 WERE EMPLOYED FOR DIRECT NOE REMARK 3 CROSS PEAKS OF STRONG, MEDIUM AND WEAK INTENSITIES, RESPECTIVELY, REMARK 3 FOR ALL CROSS PEAKS EXCEPT THOSE ASSOCIATED WITH THE REMARK 3 INTRARESIDUE H8/6-TO-H2 AND H3 INTERACTIONS. FOR THESE PROTON REMARK 3 PAIRS, UPPER DISTANCE LIMITS OF 4.2 AND 3.2 WERE THEREFORE REMARK 3 EMPLOYED FOR NOES OF MEDIUM AND STRONG INTENSITY, REMARK 3 RESPECTIVELY.43 CROSS-HELIX P-P DISTANCE RESTRAINTS (WITH 20% REMARK 3 WEIGHTING COEFFICIENT) WERE EMPLOYED FOR A-FORM HELICAL SEGMENTS REMARK 3 TO PREVENT THE GENERATION OF STRUCTURES WITH COLLAPSED MAJOR REMARK 3 GROOVES:43,52,55 P(I)-P(I+2) (CROSS-HELIX PHOSPHORUS OF THE I+2 REMARK 3 BASE PAIR) = 16.1 - 17.1 , P(I)-P(I+3) = 14.2 - 15.2 ; P(I)-P(I+ REMARK 3 4) = 11.7 -12.7 ; P(I)-P(I+5) = 9.4 -10.4 ; P(I)-P(I+6) = 9.0 - REMARK 3 10.0 . TORSION ANGLE RESTRAINTS FOR A HELICAL STEM RESIDUES WERE REMARK 3 CENTERED AROUND PUBLISHED A-FORM RNA VALUES 112 WITH ALLOWED REMARK 3 DEVIATIONS OF 50 DEGREES. FOUR RESTRAINTS PER HYDROGEN BOND WERE REMARK 3 EMPLOYED TO ENFORCE APPROXIMATELY LINEAR NH-N AND NH-O BOND REMARK 3 DISTANCES OF 1.85 0.05, AND TWO LOWER LIMIT RESTRAINTS PER BASE REMARK 3 PAIR WERE EMPLOYED TO WEAKLY ENFORCE BASE PAIR PLANARITY (20% REMARK 3 WEIGHTING COEFFICIENT) (G-C BASE PAIRS: G-C4 TO C-C6 > 8.3 AND G- REMARK 3 N9 TO C-H6 > 10.75 . A-U BASE PAIRS: A-C4 TO U-C6 > 8.3 AND A-N9 REMARK 3 TO U-H6 > 10.75 ). REMARK 4 REMARK 4 2L1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000101835. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 80 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 400-800 UM [U-2H] RNA (65-MER), REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 340 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 G A 309 O4' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 G A 309 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 G A 309 C6 - N1 - C2 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 G A 309 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 G A 309 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 310 C1' - O4' - C4' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 G A 310 C6 - N1 - C2 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 G A 310 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 310 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 311 O4' - C4' - C3' ANGL. DEV. = -10.3 DEGREES REMARK 500 1 C A 311 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 G A 312 O4' - C4' - C3' ANGL. DEV. = -9.7 DEGREES REMARK 500 1 G A 312 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 G A 312 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 312 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 312 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 313 O4' - C4' - C3' ANGL. DEV. = -8.9 DEGREES REMARK 500 1 G A 313 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 313 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 313 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 313 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 A A 314 O4' - C4' - C3' ANGL. DEV. = -10.6 DEGREES REMARK 500 1 A A 314 C1' - O4' - C4' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 C A 315 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES REMARK 500 1 C A 315 C1' - O4' - C4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 C A 316 O4' - C4' - C3' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 C A 316 C1' - O4' - C4' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 C A 317 O4' - C4' - C3' ANGL. DEV. = -9.8 DEGREES REMARK 500 1 C A 317 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 G A 318 O4' - C4' - C3' ANGL. DEV. = -8.1 DEGREES REMARK 500 1 G A 318 C1' - O4' - C4' ANGL. DEV. = 7.2 DEGREES REMARK 500 1 G A 318 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 318 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 318 C5 - C6 - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 U A 319 O4' - C4' - C3' ANGL. DEV. = -13.1 DEGREES REMARK 500 1 G A 320 O4' - C4' - C3' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 G A 320 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 320 C6 - N1 - C2 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 G A 320 N1 - C2 - N3 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 320 C5 - C6 - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 321 O4' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 G A 321 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 G A 321 C6 - N1 - C2 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 G A 321 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 G A 321 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 322 O4' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 U A 322 C1' - O4' - C4' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 G A 323 O4' - C4' - C3' ANGL. DEV. = -11.5 DEGREES REMARK 500 1 G A 323 C1' - O4' - C4' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 G A 323 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 7802 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17083 RELATED DB: BMRB DBREF1 2L1F A 309 373 GB AF033811 DBREF2 2L1F A AF033811.1 45 109 DBREF1 2L1F B 709 774 GB AF033811 DBREF2 2L1F B AF033811.1 45 110 SEQADV 2L1F A A 328 GB AF033811. U 64 ENGINEERED MUTATION SEQADV 2L1F U A 333 GB AF033811. A 69 ENGINEERED MUTATION SEQADV 2L1F A B 728 GB AF033811. U 64 ENGINEERED MUTATION SEQADV 2L1F U B 733 GB AF033811. A 69 ENGINEERED MUTATION SEQRES 1 A 65 G G C G G A C C C G U G G SEQRES 2 A 65 U G G A A C A G A C G U G SEQRES 3 A 65 U U C G G A A C A C C C G SEQRES 4 A 65 G C C G C A A C C C U G G SEQRES 5 A 65 G A G A C G U C C C A G G SEQRES 1 B 66 G G C G G A C C C G U G G SEQRES 2 B 66 U G G A A C A G A C G U G SEQRES 3 B 66 U U C G G A A C A C C C G SEQRES 4 B 66 G C C G C A A C C C U G G SEQRES 5 B 66 G A G A C G U C C C A G G SEQRES 6 B 66 G CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1